Fetal thymi from diabetes-prone but not diabetes-resistant BB/Wor rats fail to generate mature ART2+ T-cells in organ culture.

Diabetes-prone (BBDP) BB rats develop spontaneous autoimmune diabetes mellitus. They are lymphopenic and severely deficient in ART2+ T-cells. Diabetes-resistant BB (BBDR) rats do not develop spontaneous diabetes and have normal numbers of ART2+ T-cells. T-cell lymphopenia in BBDP rats results from hematopoietic stem cell defects leading to abnormal intrathymic T-cell maturation. To study this process, we established rat fetal thymic organ cultures (FTOC). Like mouse FTOC, cultures of BBDR rat thymi yielded approximately 10(5) cells per lobe. The majority of cells were CD8+ART2+ T-cells. In contrast, BBDP rat FTOC yielded 60% fewer cells (approximately 0.3 x 10(5)/lobe), a smaller percentage of CD8+ and TcRalphabeta+ T-cells, and almost no detectable ART2+ T-cells. ART2 mRNA was detectable in BBDR but not BBDP FTOC. In contrast, expression of mRNAs encoding bcl-2 and a panel of cytokines was comparable in BBDP and BBDR FTOC. Addition of anti-ICAM-1 (CD54) antibody reduced T-cell number in BBDR rat FTOC by approximately 70%, but addition of IL-7 or IL-1beta had no effect. The data demonstrate that BBDP thymocytes fail to generate mature ART2+ T-cells in rat FTOC, a system that can now be used to study the mechanism of this process.     

Predicting insect outbreaks using machine learning: A mountain pine beetle case study

Planning forest management relies on predicting insect outbreaks such as mountain pine beetle, particularly in the intermediate‐term future, e.g., 5‐year. Machine‐learning algorithms are potential solutions to this challenging problem due to their many successes across a variety of prediction tasks. However, there are many subtle challenges in applying them: identifying the best learning models and the best subset of available covariates (including time lags) and properly evaluating the models to avoid misleading performance‐measures. We systematically address these issues in predicting the chance of a mountain pine beetle outbreak in the Cypress Hills area and seek models with the best performance at predicting future 1‐, 3‐, 5‐ and 7‐year infestations. We train nine machine‐learning models, including two generalized boosted regression trees (GBM) that predict future 1‐ and 3‐year infestations with 92% and 88% AUC, and two novel mixed models that predict future 5‐ and 7‐year infestations with 86% and 84% AUC, respectively. We also consider forming the train and test datasets by splitting the original dataset randomly rather than using the appropriate year‐based approach and show that this may obtain models that score high on the test dataset but low in practice, resulting in inaccurate performance evaluations. For example, a k‐nearest neighbor model with the actual performance of 68% AUC, scores the misleadingly high 78% on a test dataset obtained from a random split, but the more accurate 66% on a year‐based split. We then investigate how the prediction accuracy varies with respect to the provided history length of the covariates and find that neural network and naive Bayes, predict more accurately as history‐length increases, particularly for future 1‐ and 3‐year predictions, and roughly the same holds with GBM. Our approach is applicable to other invasive species. The resulting predictors can be used in planning forest and pest management and planning sampling locations in field studies.     

Characterization of the lipid and protein organization in HBsAg viral particles by steady-state and time-resolved fluorescence spectroscopy

Hepatitis B surface antigen (HBsAg) particles, produced in the yeast Hansenula polymorpha, are 20 nm particles, composed of S surface viral proteins and host-derived lipids. Since the detailed structure of these particles is still missing, we further characterized them by fluorescence techniques. Fluorescence correlation spectroscopy indicated that the particles are mainly monomeric, with about 70 S proteins per particle. The S proteins were characterized through the intrinsic fluorescence of their thirteen Trp residues. Fluorescence quenching and time-resolved fluorescence experiments suggest the presence of both low emissive embedded Trp residues and more emissive Trp residues at the surface of the HBsAg particles. The low emission of the embedded Trp residues is consistent with their close proximity in alpha-helices. Furthermore, S proteins exhibit restricted movement, as expected from their tight association with lipids. The lipid organization of the particles was studied using viscosity-sensitive DPH-based probes and environment sensitive 3-hydroxyflavone probes, and compared to lipid vesicles and low density lipoproteins (LDLs), taken as models. Like LDLs, the HBsAg particles were found to be composed of an ordered rigid lipid interface, probably organized as a phospholipid monolayer, and a more hydrophobic and fluid inner core, likely composed of triglycerides and free fatty acids. However, the lipid core of HBsAg particles was substantially more polar than the LDL one, probably due to its larger content in proteins and its lower content in sterols. Based on our data, we propose a structural model for HBsAg particles where the S proteins deeply penetrate into the lipid core.     

Systematic Approach to Solvent Selection for Biphasic Systems with a Combination of COSMO‐RS and a Dynamic Modeling Tool

Biphasic aqueous‐organic systems are important reaction systems for catalytic processes. This is especially true for biocatalysis where the range of accessible products can be significantly extended. In such systems, the aqueous phase is the reactive phase in which the biocatalyst is dissolved and the organic phase is nonreactive and acts as substrate reservoir and as in situ product extraction solvent. Here, the choice of the nonreactive phase is highly important for the overall performance of the system. In this contribution, a systematic approach to solvent selection for biphasic aqueous‐organic systems is presented with respect to partition coefficients. The model reaction is the stereoselective carbon‐carbon coupling of two 3,5‐dimethoxy‐benzaldehyde molecules to (R)‐3,3',5,5'‐tetramethoxy‐benzoin catalyzed by benzaldehyde lyase (EC 4.1.2.38) from Pseudomonas fluorescens. A systematic approach to solvent selection consisting of two steps is proposed: Firstly, the conductor‐like screening model for real solvents (COSMO‐RS) is used to facilitate a fast solvent screening. Since this is an ab initio approach it allows a pre‐screening without laborious experimental input. The proposed ranking of solvents, based on the ratio of partition coefficients at infinite dilution, is a sound basis for the successive steps. Secondly, a dynamic model is fitted to experimental data in order to obtain detailed and reliable results for mass transfer and partition coefficients. Therefore, the method makes efficient use of the experimental data and substantiates quantitative results with guided experiments.     

A temporospatial map of adhesive molecules in the organ of corti of the mouse cochlea

In the nervous system, several classes of cell-surface and extracellular matrix molecules have been implicated in processes such as neural growth, fasciculation, pathfinding, target recognition and synaptogenesis, which require cell-to-cell or cell-to-substrate binding. In the developing mouse cochlea, little is known about the types of cell-surface and extracellular matrix molecules existing along the neural growth paths or their possible roles in development. Whole mount and sectioned cochlear tissue were immunolabeled for six different adhesive molecules - neural cell adhesion molecule (NCAM), polysialic acid (PSA), neural cell adhesion molecule L1, E-cadherin, syndecan-1 and tenascin-C. A temporospatial map of adhesive molecule distribution in the basal turns of the mouse cochlea was generated. Distributions of adhesive molecules were compared to each other and to the known progress of neural development in the region. This comparison demonstrated differences in the complements of adhesive molecules between the inner and outer hair cell regions, and variations in the expressions of adhesion molecules among different types of nerve fibers. In addition, developmental changes in the adhesive environment around and beneath the outer hair cells coincided with the known timing of the appearance of morphologically defined efferent synapses. These observations raise the possibility that molecular differences at the cell surface of inner and outer hair cells are one way that ingrowing neurites distinguish different environments to determine their growth routes and synaptic partners in the cochlea. In addition these observations demonstrate the potential for differential signaling of afferent and efferent innervation by altering the microenvironments in which synapses are formed.     

Interspecific differences in hematozoan infection in Sonoran desert Aimophila sparrows

Numerous studies have identified factors that control avian hematozoan infections, but the mechanisms that account for host differences in parasitemia remain largely speculative. To address this issue, we compared the prevalence of these parasites in stained blood smears from four conspecific Sonoran desert Aimophila sparrow species sampled during their breeding season: rufous-winged (Aimophila carpalis; RWSP), rufous-crowned (Aimophila ruficeps; RCSP), Cassin's (Aimophila cassinii, CASP), and Botteri's (Aimophila botterii; BOSP) sparrows. Blood smears contained Haemoproteus fringillae (RWSP), Trypanosoma everetti (RWSP, RCSP, BOSP), Trypanosoma avium (CASP), and microfilariae (all species). Most (92.5%) RWSP (n=40) were infected with Haemoproteus, but this parasite was not detected in RCSP (n=20) or BOSP (n=20) and was found only in one (2.5%) CASP (n=40). Trypanosoma spp. and microfilariae were detected in all species, but prevalence differed between these four sparrow species. Species differences in parasite prevalence were not due to difference in sex, age, adult body mass, incubation period, breeding habitat, or plumage colorfulness. However, differences in Haemoproteus sp. prevalence correlated with preferred nesting height, as RWSP generally nest above ground, whereas the other species nest on or close to the ground. Elevated H. fringillae prevalence in breeding-condition RWSP presumably does not result from a seasonal relapse associated with breeding or require new infection because 1) this prevalence did not differ in males sampled during and outside (n=21) the breeding season, and 2) all male RWSP (n=25) that we held in captivity and shielded from new infections and influence of natural photoperiod for 1 yr had viable blood H. fringillae gametocytes. H. fringillae prevalence in fall-sampled hatch-year male RWSP (n=11) was 63.6%, demonstrating that this parasite can be transmitted on the breeding grounds and during the first months of life. T. everetti prevalence in RWSP was lower in winter than in summer and also in long-term captive than in free-ranging adults. Presence of this parasite in the blood of breeding males may depend on recrudescence of existing infections or new infections.     

Haemoproteids of the avian family Dicruridae (the drongos)

Dicrurids are a widespread avian family in Africa and Asia. Earlier surveys of this family in these areas have reported the presence of hematozoa and 1 species of Haemoproteus, i.e., Haemoproteus dicruri (De Mello, 1935). One species of drongo occurs in Madagascar and has not been examined previously. Blood smears collected from wild-caught crested drongos, Dicrurus forficatus, in Madagascar were examined using a compound microscope for the presence of hematozoa. A new species, Haemoproteus khani, is described in this study. This new species has circumnuclear gametocytes, in contrast to the halteridial H. dicruri. In addition, H. dicruri is reported for the first time from the crested drongo and is redescribed. This is the first report of hematozoa in drongos of Madagascar.     

Gastrointestinal parasites of the colobus monkeys of Uganda

From August 1997 to July 2003, we collected 2,103 fecal samples from free-ranging individuals of the 3 colobus monkey species of Uganda-the endangered red colobus (Piliocolobus tephrosceles), the eastern black-and-white colobus (Colobus guereza), and the Angolan black-and-white colobus (C. angolensis)--to identify and determine the prevalence of gastrointestinal parasites. Helminth eggs, larvae, and protozoan cysts were isolated by sodium nitrate flotation and fecal sedimentation. Coprocultures facilitated identification of helminths. Seven nematodes (Strongyloides fulleborni, S. stercoralis, Oesophagostomum sp., an unidentified strongyle, Trichuris sp., Ascaris sp., and Colobenterobius sp.), 1 cestode (Bertiella sp.), 1 trematode (Dicrocoeliidae), and 3 protozoans (Entamoeba coli, E. histolytica, and Giardia lamblia) were detected. Seasonal patterns of infection were not apparent for any parasite species infecting colobus monkeys. Prevalence of S. fulleborni was higher in adult male compared to adult female red colobus, but prevalence did not differ for any other shared parasite species between age and sex classes.     

A new species of Plasmodium from Malagasy vangas

During a recent examination of blood smears from Malagasy birds, a species of avian Plasmodium unlike those currently known was observed. All infected birds were members of the Vangidae, which is endemic to Madagascar and the Comoro Islands. Plasmodium parvulum n. sp. is described, and classified as a member of the subgenus Haemamoeba because of gametocyte and schizont shape, displacement of the host cell nucleus, as well as distortion of the host cell. Round, rosettelike schizonts with 6-8 merozoites, clumped refractile granules, and little cytoplasm were observed. Both schizonts and mature, round gametocytes rotated and displaced the erythrocyte nucleus. A brief comparison to P. relictum is included.     

Blockade of CD40-mediated signaling is sufficient for inducing islet but not skin transplantation tolerance

Treatment of mice with a single donor-specific transfusion (DST) plus a brief course of anti-CD154 mAb to block CD40-mediated signaling uniformly induces donor-specific transplantation tolerance. Survival of islet allografts in treated mice is permanent, but skin grafts eventually fail unless recipients are thymectomized. The nature of the cellular mechanisms involved and the basis for the difference in survival of islet vs skin allografts are not known. In this study, we used CD40 knockout mice to investigate the role of CD40-mediated signaling in each component of the tolerance induction protocol: the DST, the graft, and the host. When CD40-mediated signaling was eliminated in only the DST or the graft, islet allografts were rapidly rejected. However, when CD40 signaling was eliminated in the host, approximately 40% of the islet allografts survived. When CD40 signaling was eliminated in the DST, the graft, and the host, islet grafts survived long term (>84 days), whereas skin allografts were rapidly rejected ( approximately 13 days). We conclude that transplantation tolerance induction in mice treated with DST and anti-CD154 mAb requires blockade of CD40-mediated signaling in the DST, the graft, and the host. Blockade of CD40-mediated signaling is necessary and sufficient for inducing islet allograft tolerance and is necessary but not sufficient for long-term skin allograft survival. We speculate that a requirement for regulatory CD4(+) T cells in skin allograft recipients could account for this differential response to tolerance induction.